Starting phenix.real_space_refine
on Fri Oct 10 11:05:57 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jys_36730/10_2025/8jys_36730.map"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.042
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2271      2.51       5
     N     587      2.21       5
     O     648      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3522
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 31, 241
          Classifications: {'peptide': 31}
          Link IDs: {'PTRANS': 1, 'TRANS': 29}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 253
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 253
          Classifications: {'peptide': 32}
          Link IDs: {'PTRANS': 1, 'TRANS': 30}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 1514
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 189, 1514
          Classifications: {'peptide': 189}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 176}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.17, per 1000 atoms: 0.33
  Number of scatterers: 3522
  At special positions: 0
  Unit cell: (90.094, 67.36, 119.564, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     648      8.00
     N     587      7.00
     C    2271      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 391 " - pdb=" SG  CYS D 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 480 " - pdb=" SG  CYS D 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 99.0 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  822

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 5 sheets defined
      11.8% alpha, 12.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.11
  Creating SS restraints...
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 383 through 390
      removed outlier: 4.391A  pdb=" N   LEU B 390 " --> pdb=" O   LYS B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
      removed outlier: 4.104A  pdb=" N   ILE B 410 " --> pdb=" O   GLU B 406 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ALA B 411 " --> pdb=" O   VAL B 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 406 through 411'
    Processing helix  chain 'D' and resid 338 through 343
    Processing helix  chain 'D' and resid 365 through 370
    Processing helix  chain 'D' and resid 383 through 388
    Processing helix  chain 'D' and resid 404 through 410
      removed outlier: 3.808A  pdb=" N   VAL D 407 " --> pdb=" O   GLY D 404 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE B 402 " --> pdb=" O   TYR B 508 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 356 through 358
      removed outlier: 3.709A  pdb=" N   VAL B 395 " --> pdb=" O   ILE B 358 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLU B 516 " --> pdb=" O   ASN B 394 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 453
    Processing sheet with id=AA4, first strand: chain 'D' and resid 356 through 358
      removed outlier: 4.195A  pdb=" N   VAL D 395 " --> pdb=" O   ILE D 358 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'D' and resid 473 through 474
      removed outlier: 3.969A  pdb=" N   TYR D 489 " --> pdb=" O   TYR D 473 " (cutoff:3.500A)

    56 hydrogen bonds defined for protein.
    129 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.51

  Time building geometry restraints manager: 0.32 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1112
        1.34 -     1.47: 1024
        1.47 -     1.59: 1473
        1.59 -     1.72: 0
        1.72 -     1.84: 16
  Bond restraints: 3625
  Sorted by residual:
  bond pdb=" N   LEU C 109 "
       pdb=" CA  LEU C 109 "
    ideal  model  delta    sigma   weight residual
    1.461  1.496 -0.035 1.49e-02 4.50e+03 5.38e+00
  bond pdb=" C   GLU A  57 "
       pdb=" N   PRO A  58 "
    ideal  model  delta    sigma   weight residual
    1.328  1.353 -0.025 1.26e-02 6.30e+03 3.84e+00
  bond pdb=" C   ALA D 520 "
       pdb=" N   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.332  1.355 -0.023 1.33e-02 5.65e+03 3.07e+00
  bond pdb=" C   PRO B 373 "
       pdb=" O   PRO B 373 "
    ideal  model  delta    sigma   weight residual
    1.235  1.218  0.017 1.30e-02 5.92e+03 1.81e+00
  bond pdb=" C   PRO D 521 "
       pdb=" O   PRO D 521 "
    ideal  model  delta    sigma   weight residual
    1.233  1.218  0.015 1.23e-02 6.61e+03 1.46e+00
  ... (remaining 3620 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 4704
        2.01 -     4.03: 179
        4.03 -     6.04: 33
        6.04 -     8.06: 11
        8.06 -    10.07: 3
  Bond angle restraints: 4930
  Sorted by residual:
  angle pdb=" C   ASN D 422 "
        pdb=" N   TYR D 423 "
        pdb=" CA  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     121.54  131.56  -10.02 1.91e+00 2.74e-01 2.75e+01
  angle pdb=" CA  TYR D 423 "
        pdb=" CB  TYR D 423 "
        pdb=" CG  TYR D 423 "
      ideal   model   delta    sigma   weight residual
     113.90  120.74   -6.84 1.80e+00 3.09e-01 1.44e+01
  angle pdb=" N   SER B 366 "
        pdb=" CA  SER B 366 "
        pdb=" C   SER B 366 "
      ideal   model   delta    sigma   weight residual
     113.43  108.71    4.72 1.26e+00 6.30e-01 1.40e+01
  angle pdb=" CB  LYS B 356 "
        pdb=" CG  LYS B 356 "
        pdb=" CD  LYS B 356 "
      ideal   model   delta    sigma   weight residual
     111.30  119.15   -7.85 2.30e+00 1.89e-01 1.16e+01
  angle pdb=" C   GLU B 465 "
        pdb=" CA  GLU B 465 "
        pdb=" CB  GLU B 465 "
      ideal   model   delta    sigma   weight residual
     113.37  108.12    5.25 1.61e+00 3.86e-01 1.06e+01
  ... (remaining 4925 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.01: 1704
       16.01 -    32.01: 307
       32.01 -    48.02: 81
       48.02 -    64.02: 20
       64.02 -    80.02: 6
  Dihedral angle restraints: 2118
    sinusoidal: 826
      harmonic: 1292
  Sorted by residual:
  dihedral pdb=" CB  CYS B 480 "
           pdb=" SG  CYS B 480 "
           pdb=" SG  CYS B 488 "
           pdb=" CB  CYS B 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -21.65  -64.35     1      1.00e+01 1.00e-02 5.44e+01
  dihedral pdb=" CB  CYS B 336 "
           pdb=" SG  CYS B 336 "
           pdb=" SG  CYS B 361 "
           pdb=" CB  CYS B 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   46.59   46.41     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CB  CYS D 379 "
           pdb=" SG  CYS D 379 "
           pdb=" SG  CYS D 432 "
           pdb=" CB  CYS D 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   52.27   40.73     1      1.00e+01 1.00e-02 2.33e+01
  ... (remaining 2115 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 272
       0.031 -    0.061: 132
       0.061 -    0.092: 71
       0.092 -    0.123: 30
       0.123 -    0.153: 4
  Chirality restraints: 509
  Sorted by residual:
  chirality pdb=" CA  ILE B 434 "
            pdb=" N   ILE B 434 "
            pdb=" C   ILE B 434 "
            pdb=" CB  ILE B 434 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.15 2.00e-01 2.50e+01 5.87e-01
  chirality pdb=" CA  VAL D 511 "
            pdb=" N   VAL D 511 "
            pdb=" C   VAL D 511 "
            pdb=" CB  VAL D 511 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.15 2.00e-01 2.50e+01 5.68e-01
  chirality pdb=" CA  ILE B 402 "
            pdb=" N   ILE B 402 "
            pdb=" C   ILE B 402 "
            pdb=" CB  ILE B 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  ... (remaining 506 not shown)

  Planarity restraints: 644
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA D 372 "    0.053 5.00e-02 4.00e+02   7.93e-02 1.01e+01
        pdb=" N   PRO D 373 "   -0.137 5.00e-02 4.00e+02
        pdb=" CA  PRO D 373 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO D 373 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C  57 "    0.043 5.00e-02 4.00e+02   6.63e-02 7.04e+00
        pdb=" N   PRO C  58 "   -0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO C  58 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO C  58 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D 509 "   -0.184 9.50e-02 1.11e+02   8.27e-02 4.24e+00
        pdb=" NE  ARG D 509 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG D 509 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG D 509 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG D 509 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 641 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 349
        2.74 -     3.28: 3830
        3.28 -     3.82: 5469
        3.82 -     4.36: 6023
        4.36 -     4.90: 9633
  Nonbonded interactions: 25304
  Sorted by model distance:
  nonbonded pdb=" O   PHE D 347 "
            pdb=" OH  TYR D 451 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OG  SER D 383 "
            pdb=" NZ  LYS D 386 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OG  SER D 438 "
            pdb=" OD1 ASP D 442 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" NZ  LYS D 478 "
            pdb=" O   PRO D 479 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OD2 ASP B 398 "
            pdb=" OH  TYR B 423 "
     model   vdw
     2.245 3.040
  ... (remaining 25299 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = (chain 'C' and resid 49 through 116)
}
ncs_group {
  reference = chain 'B'
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.390
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7262
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3633  Z= 0.199
  Angle     :  0.969  10.071   4946  Z= 0.518
  Chirality :  0.048   0.153    509
  Planarity :  0.008   0.083    644
  Dihedral  : 17.514  80.024   1272
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.71 %
    Favored  : 86.12 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 38.34 %
    Favored  : 59.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.49 (0.38), residues: 425
  helix: -2.42 (0.72), residues: 44
  sheet: -0.81 (0.64), residues: 68
  loop : -2.90 (0.32), residues: 313

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG B 346 
 TYR   0.022   0.002   TYR B 508 
 PHE   0.029   0.002   PHE B 456 
 TRP   0.022   0.003   TRP B 436 
 HIS   0.001   0.000   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 3625)
  covalent geometry    : angle       0.96358 ( 4930)
  SS BOND              : bond        0.00352 (    8)
  SS BOND              : angle       2.06712 (   16)
  hydrogen bonds       : bond        0.20907 (   53)
  hydrogen bonds       : angle       7.89847 (  129)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  374 PHE cc_start: 0.7908 (t80) cc_final: 0.7666 (m-80)
REVERT: B  451 TYR cc_start: 0.7749 (m-80) cc_final: 0.7514 (m-80)
REVERT: D  516 GLU cc_start: 0.7900 (tp30) cc_final: 0.7482 (tm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 105
  average time/residue: 0.1005
  time to fit residues: 12.1902
Evaluate side-chains
  102 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 26 optimal weight:    5.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 32 optimal weight:    0.2980
   chunk 31 optimal weight:    4.9990
   chunk 25 optimal weight:    8.9990
   chunk 19 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:   20.0000
   chunk 37 optimal weight:    6.9990
   overall best weight:    1.8384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 481 ASN
D 422 ASN
D 474 GLN
D 481 ASN
D 487 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.117803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.098272 restraints weight = 13027.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.101377 restraints weight = 7988.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.103637 restraints weight = 5529.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.105133 restraints weight = 4150.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.106268 restraints weight = 3329.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3612
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.154
  Angle     :  0.766  11.964   4946  Z= 0.386
  Chirality :  0.046   0.164    509
  Planarity :  0.007   0.053    644
  Dihedral  :  5.654  20.121    492
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 12.30
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 11.76 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  :  5.36 %
    Favored  : 93.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.23 (0.38), residues: 425
  helix: -3.51 (0.50), residues: 46
  sheet: -0.46 (0.63), residues: 64
  loop : -2.50 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 509 
 TYR   0.023   0.002   TYR B 423 
 PHE   0.024   0.002   PHE D 375 
 TRP   0.009   0.001   TRP D 436 
 HIS   0.006   0.002   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 ( 3625)
  covalent geometry    : angle       0.75874 ( 4930)
  SS BOND              : bond        0.00515 (    8)
  SS BOND              : angle       2.03932 (   16)
  hydrogen bonds       : bond        0.03862 (   53)
  hydrogen bonds       : angle       6.83901 (  129)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 124
  time to evaluate  : 0.111 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  403 ARG cc_start: 0.7534 (mtt180) cc_final: 0.7316 (mtt90)
REVERT: D  402 ILE cc_start: 0.9015 (tp) cc_final: 0.8742 (tp)
REVERT: D  472 ILE cc_start: 0.8662 (tp) cc_final: 0.8355 (tp)
REVERT: D  473 TYR cc_start: 0.8964 (t80) cc_final: 0.8478 (t80)
REVERT: D  516 GLU cc_start: 0.8416 (tp30) cc_final: 0.7490 (tm-30)
  outliers start: 3
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0816
  time to fit residues: 12.1377
Evaluate side-chains
  103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 28 optimal weight:    9.9990
   chunk 33 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 26 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   chunk 5 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   overall best weight:    1.2186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.118095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.098283 restraints weight = 12980.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.101401 restraints weight = 8013.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.103675 restraints weight = 5568.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.105239 restraints weight = 4183.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106312 restraints weight = 3341.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7143
moved from start:          0.3796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   3633  Z= 0.130
  Angle     :  0.712  10.867   4946  Z= 0.358
  Chirality :  0.046   0.179    509
  Planarity :  0.005   0.043    644
  Dihedral  :  5.435  19.154    492
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.15
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 12.00 %
    Favored  : 87.06 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.22 %
    Favored  : 96.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.10 (0.38), residues: 425
  helix: -2.94 (0.56), residues: 52
  sheet: -0.48 (0.60), residues: 69
  loop : -2.47 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 493 
 TYR   0.020   0.001   TYR B 423 
 PHE   0.017   0.002   PHE D 375 
 TRP   0.008   0.001   TRP D 436 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 3625)
  covalent geometry    : angle       0.70970 ( 4930)
  SS BOND              : bond        0.00361 (    8)
  SS BOND              : angle       1.24730 (   16)
  hydrogen bonds       : bond        0.03542 (   53)
  hydrogen bonds       : angle       6.63580 (  129)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 138
  time to evaluate  : 0.082 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 ASP cc_start: 0.7316 (p0) cc_final: 0.6982 (t70)
REVERT: B  388 ASN cc_start: 0.7045 (t0) cc_final: 0.6601 (m110)
REVERT: B  471 GLU cc_start: 0.9076 (tp30) cc_final: 0.8822 (tp30)
REVERT: D  335 LEU cc_start: 0.8966 (mm) cc_final: 0.8729 (tp)
REVERT: D  394 ASN cc_start: 0.9156 (t0) cc_final: 0.8294 (p0)
REVERT: D  402 ILE cc_start: 0.9084 (tp) cc_final: 0.8841 (tp)
REVERT: D  425 LEU cc_start: 0.9062 (pp) cc_final: 0.8851 (pp)
REVERT: D  462 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8844 (mtmm)
REVERT: D  472 ILE cc_start: 0.8228 (tp) cc_final: 0.8026 (tp)
REVERT: D  473 TYR cc_start: 0.8885 (t80) cc_final: 0.8567 (t80)
REVERT: D  516 GLU cc_start: 0.8025 (tp30) cc_final: 0.6923 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 139
  average time/residue: 0.0885
  time to fit residues: 14.2448
Evaluate side-chains
  103 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 12 optimal weight:    8.9990
   chunk 13 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0980
   chunk 21 optimal weight:   20.0000
   chunk 41 optimal weight:    6.9990
   chunk 6 optimal weight:    1.9990
   overall best weight:    2.6188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.092810 restraints weight = 13200.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.095719 restraints weight = 8220.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.097708 restraints weight = 5755.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.099195 restraints weight = 4392.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.100217 restraints weight = 3536.708|
|-----------------------------------------------------------------------------|
r_work (final): 0.3516
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3633  Z= 0.167
  Angle     :  0.734  10.491   4946  Z= 0.376
  Chirality :  0.047   0.161    509
  Planarity :  0.006   0.048    644
  Dihedral  :  5.680  18.613    492
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  0.94 %
    Allowed  : 13.41 %
    Favored  : 85.65 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  3.75 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.09 (0.39), residues: 425
  helix: -2.72 (0.60), residues: 51
  sheet: -0.59 (0.59), residues: 68
  loop : -2.47 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 403 
 TYR   0.017   0.002   TYR B 453 
 PHE   0.022   0.002   PHE B 456 
 TRP   0.010   0.001   TRP A  53 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 3625)
  covalent geometry    : angle       0.73089 ( 4930)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       1.42272 (   16)
  hydrogen bonds       : bond        0.03676 (   53)
  hydrogen bonds       : angle       6.71535 (  129)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  453 TYR cc_start: 0.8323 (t80) cc_final: 0.7912 (t80)
REVERT: B  471 GLU cc_start: 0.9090 (tp30) cc_final: 0.8863 (tp30)
REVERT: B  517 LEU cc_start: 0.8682 (mp) cc_final: 0.8444 (tt)
REVERT: C  106 TYR cc_start: 0.5856 (p90) cc_final: 0.5577 (p90)
REVERT: D  335 LEU cc_start: 0.8980 (mm) cc_final: 0.8741 (tp)
REVERT: D  340 GLU cc_start: 0.9126 (mp0) cc_final: 0.8859 (mp0)
REVERT: D  386 LYS cc_start: 0.8605 (pttt) cc_final: 0.8327 (pttp)
REVERT: D  394 ASN cc_start: 0.9206 (t0) cc_final: 0.8076 (p0)
REVERT: D  401 VAL cc_start: 0.8731 (m) cc_final: 0.8293 (m)
REVERT: D  402 ILE cc_start: 0.9077 (tp) cc_final: 0.8735 (tp)
REVERT: D  406 GLU cc_start: 0.9057 (pm20) cc_final: 0.8619 (pm20)
REVERT: D  409 GLN cc_start: 0.8835 (mt0) cc_final: 0.8491 (tt0)
REVERT: D  425 LEU cc_start: 0.9097 (pp) cc_final: 0.8896 (pp)
REVERT: D  472 ILE cc_start: 0.7796 (tp) cc_final: 0.6392 (tp)
REVERT: D  473 TYR cc_start: 0.8911 (t80) cc_final: 0.8524 (t80)
REVERT: D  478 LYS cc_start: 0.9003 (tptp) cc_final: 0.8795 (tptt)
REVERT: D  516 GLU cc_start: 0.8098 (tp30) cc_final: 0.6900 (tm-30)
  outliers start: 1
  outliers final: 1
  residues processed: 133
  average time/residue: 0.0845
  time to fit residues: 13.1826
Evaluate side-chains
  100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 16 optimal weight:    8.9990
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    8.9990
   chunk 26 optimal weight:    0.4980
   chunk 13 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 2 optimal weight:   10.0000
   chunk 32 optimal weight:    0.4980
   chunk 8 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0970
   chunk 37 optimal weight:    7.9990
   overall best weight:    2.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 505 HIS
D 487 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.111522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.091809 restraints weight = 13076.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094634 restraints weight = 8235.421|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.096659 restraints weight = 5836.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.098085 restraints weight = 4477.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.099026 restraints weight = 3636.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.3507
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7318
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3633  Z= 0.172
  Angle     :  0.762  11.630   4946  Z= 0.388
  Chirality :  0.048   0.183    509
  Planarity :  0.006   0.052    644
  Dihedral  :  5.964  21.897    492
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 14.93
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 12.71 %
    Favored  : 86.12 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  4.83 %
    Favored  : 94.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.07 (0.39), residues: 425
  helix: -2.52 (0.66), residues: 46
  sheet: -0.57 (0.61), residues: 70
  loop : -2.52 (0.34), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 493 
 TYR   0.019   0.002   TYR B 508 
 PHE   0.031   0.002   PHE B 375 
 TRP   0.008   0.001   TRP D 436 
 HIS   0.001   0.001   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 3625)
  covalent geometry    : angle       0.75959 ( 4930)
  SS BOND              : bond        0.00331 (    8)
  SS BOND              : angle       1.37970 (   16)
  hydrogen bonds       : bond        0.03389 (   53)
  hydrogen bonds       : angle       6.78808 (  129)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 125
  time to evaluate  : 0.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8217 (pm20) cc_final: 0.7065 (tp30)
REVERT: B  423 TYR cc_start: 0.8697 (t80) cc_final: 0.8336 (t80)
REVERT: B  453 TYR cc_start: 0.8501 (t80) cc_final: 0.7965 (t80)
REVERT: B  493 ARG cc_start: 0.8326 (ttm-80) cc_final: 0.8079 (tpp80)
REVERT: D  335 LEU cc_start: 0.8943 (mm) cc_final: 0.8740 (tp)
REVERT: D  340 GLU cc_start: 0.9078 (mp0) cc_final: 0.8829 (mp0)
REVERT: D  394 ASN cc_start: 0.9086 (t0) cc_final: 0.7942 (p0)
REVERT: D  402 ILE cc_start: 0.9146 (tp) cc_final: 0.8779 (tp)
REVERT: D  406 GLU cc_start: 0.8980 (pm20) cc_final: 0.8644 (pm20)
REVERT: D  425 LEU cc_start: 0.9182 (pp) cc_final: 0.8966 (pp)
REVERT: D  473 TYR cc_start: 0.9138 (t80) cc_final: 0.8863 (t80)
REVERT: D  478 LYS cc_start: 0.8999 (tptp) cc_final: 0.8777 (tptt)
REVERT: D  486 PHE cc_start: 0.7769 (t80) cc_final: 0.7531 (t80)
REVERT: D  506 GLN cc_start: 0.8424 (mt0) cc_final: 0.8175 (mt0)
REVERT: D  516 GLU cc_start: 0.8025 (tp30) cc_final: 0.6870 (tm-30)
  outliers start: 1
  outliers final: 0
  residues processed: 125
  average time/residue: 0.0803
  time to fit residues: 11.8934
Evaluate side-chains
  99 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.134 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:   10.0000
   chunk 29 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    3.9990
   chunk 35 optimal weight:    7.9990
   chunk 27 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.111302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092163 restraints weight = 13209.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.094968 restraints weight = 8241.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.097000 restraints weight = 5778.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.098464 restraints weight = 4371.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.099537 restraints weight = 3527.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3512
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7311
moved from start:          0.5069

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3633  Z= 0.153
  Angle     :  0.714  11.345   4946  Z= 0.361
  Chirality :  0.046   0.190    509
  Planarity :  0.005   0.045    644
  Dihedral  :  5.708  19.780    492
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.61
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.41 %
    Favored  : 85.41 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  2.14 %
    Favored  : 97.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.14 (0.38), residues: 425
  helix: -2.54 (0.63), residues: 52
  sheet: -0.51 (0.59), residues: 72
  loop : -2.61 (0.34), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 493 
 TYR   0.018   0.002   TYR B 453 
 PHE   0.022   0.002   PHE D 400 
 TRP   0.009   0.001   TRP D 436 
 HIS   0.001   0.001   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 ( 3625)
  covalent geometry    : angle       0.71120 ( 4930)
  SS BOND              : bond        0.00294 (    8)
  SS BOND              : angle       1.37258 (   16)
  hydrogen bonds       : bond        0.03438 (   53)
  hydrogen bonds       : angle       6.67584 (  129)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 0.084 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8260 (pm20) cc_final: 0.7056 (tp30)
REVERT: B  517 LEU cc_start: 0.8922 (mp) cc_final: 0.8231 (tt)
REVERT: D  340 GLU cc_start: 0.9036 (mp0) cc_final: 0.8775 (mp0)
REVERT: D  394 ASN cc_start: 0.9059 (t0) cc_final: 0.8265 (p0)
REVERT: D  402 ILE cc_start: 0.9088 (tp) cc_final: 0.8708 (tp)
REVERT: D  406 GLU cc_start: 0.8988 (pm20) cc_final: 0.8620 (pm20)
REVERT: D  473 TYR cc_start: 0.9059 (t80) cc_final: 0.8805 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0837
  time to fit residues: 12.6545
Evaluate side-chains
  100 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 25 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 11 optimal weight:    4.9990
   chunk 22 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 38 optimal weight:    8.9990
   chunk 2 optimal weight:    6.9990
   chunk 20 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    2.9788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
B 422 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.109237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.089814 restraints weight = 13402.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.092696 restraints weight = 8356.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.094722 restraints weight = 5865.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.096107 restraints weight = 4459.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.097193 restraints weight = 3603.314|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.5444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3633  Z= 0.177
  Angle     :  0.747  11.205   4946  Z= 0.383
  Chirality :  0.048   0.202    509
  Planarity :  0.005   0.056    644
  Dihedral  :  6.022  20.194    492
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 14.59 %
    Favored  : 84.24 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.61 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.38), residues: 425
  helix: -2.69 (0.60), residues: 53
  sheet: -0.77 (0.58), residues: 69
  loop : -2.69 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 493 
 TYR   0.023   0.002   TYR B 453 
 PHE   0.033   0.002   PHE B 375 
 TRP   0.009   0.002   TRP D 436 
 HIS   0.002   0.001   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 3625)
  covalent geometry    : angle       0.74171 ( 4930)
  SS BOND              : bond        0.00411 (    8)
  SS BOND              : angle       1.67359 (   16)
  hydrogen bonds       : bond        0.03786 (   53)
  hydrogen bonds       : angle       6.96875 (  129)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8455 (pm20) cc_final: 0.7367 (tp30)
REVERT: B  489 TYR cc_start: 0.7836 (m-80) cc_final: 0.7613 (m-80)
REVERT: D  340 GLU cc_start: 0.9039 (mp0) cc_final: 0.8782 (mp0)
REVERT: D  394 ASN cc_start: 0.9121 (t0) cc_final: 0.8293 (p0)
REVERT: D  402 ILE cc_start: 0.9110 (tp) cc_final: 0.8830 (tp)
REVERT: D  406 GLU cc_start: 0.8960 (pm20) cc_final: 0.8476 (pm20)
REVERT: D  409 GLN cc_start: 0.8826 (mt0) cc_final: 0.8544 (tt0)
REVERT: D  473 TYR cc_start: 0.9019 (t80) cc_final: 0.8619 (t80)
REVERT: D  509 ARG cc_start: 0.8274 (ttm110) cc_final: 0.7878 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 120
  average time/residue: 0.0839
  time to fit residues: 11.8432
Evaluate side-chains
  101 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 7 optimal weight:   10.0000
   chunk 36 optimal weight:    5.9990
   chunk 39 optimal weight:   10.0000
   chunk 37 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 19 optimal weight:    0.2980
   chunk 30 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    6.9990
   overall best weight:    3.0186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.108127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.089715 restraints weight = 13849.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.092401 restraints weight = 8645.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.094343 restraints weight = 6088.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.095706 restraints weight = 4625.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.096792 restraints weight = 3744.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.5666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   3633  Z= 0.175
  Angle     :  0.752  11.802   4946  Z= 0.384
  Chirality :  0.047   0.196    509
  Planarity :  0.005   0.053    644
  Dihedral  :  5.942  20.763    492
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 15.52
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 14.82 %
    Favored  : 84.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.39), residues: 425
  helix: -3.06 (0.61), residues: 47
  sheet: -0.83 (0.59), residues: 73
  loop : -2.63 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 493 
 TYR   0.026   0.002   TYR D 501 
 PHE   0.017   0.002   PHE D 400 
 TRP   0.010   0.002   TRP D 436 
 HIS   0.002   0.001   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 3625)
  covalent geometry    : angle       0.74712 ( 4930)
  SS BOND              : bond        0.00319 (    8)
  SS BOND              : angle       1.73998 (   16)
  hydrogen bonds       : bond        0.03723 (   53)
  hydrogen bonds       : angle       7.09301 (  129)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8506 (pm20) cc_final: 0.7378 (tp30)
REVERT: B  354 ASN cc_start: 0.9203 (t0) cc_final: 0.8840 (t0)
REVERT: B  356 LYS cc_start: 0.9200 (tppt) cc_final: 0.8655 (tppt)
REVERT: B  423 TYR cc_start: 0.8720 (t80) cc_final: 0.8355 (t80)
REVERT: B  489 TYR cc_start: 0.7858 (m-80) cc_final: 0.7615 (m-80)
REVERT: D  340 GLU cc_start: 0.9024 (mp0) cc_final: 0.8760 (mp0)
REVERT: D  394 ASN cc_start: 0.9038 (t0) cc_final: 0.8209 (p0)
REVERT: D  402 ILE cc_start: 0.9104 (tp) cc_final: 0.8805 (tp)
REVERT: D  406 GLU cc_start: 0.8945 (pm20) cc_final: 0.8469 (pm20)
REVERT: D  473 TYR cc_start: 0.9014 (t80) cc_final: 0.8621 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.0824
  time to fit residues: 12.0125
Evaluate side-chains
  96 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 20 optimal weight:    6.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 21 optimal weight:   20.0000
   chunk 26 optimal weight:    8.9990
   chunk 2 optimal weight:    7.9990
   chunk 40 optimal weight:    8.9990
   chunk 18 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 9 optimal weight:    4.9990
   chunk 27 optimal weight:    4.9990
   overall best weight:    3.7788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 360 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.106330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.088395 restraints weight = 13805.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.091022 restraints weight = 8616.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.092846 restraints weight = 6066.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.094207 restraints weight = 4625.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.095129 restraints weight = 3739.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.5973

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066   3633  Z= 0.213
  Angle     :  0.806  11.619   4946  Z= 0.414
  Chirality :  0.050   0.216    509
  Planarity :  0.005   0.054    644
  Dihedral  :  6.364  24.647    492
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 16.24 %
    Favored  : 82.59 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  1.07 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.39), residues: 425
  helix: -3.33 (0.58), residues: 47
  sheet: -1.05 (0.59), residues: 73
  loop : -2.60 (0.35), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 403 
 TYR   0.021   0.002   TYR B 495 
 PHE   0.030   0.003   PHE B 375 
 TRP   0.014   0.002   TRP B 436 
 HIS   0.003   0.001   HIS D 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 ( 3625)
  covalent geometry    : angle       0.79858 ( 4930)
  SS BOND              : bond        0.00826 (    8)
  SS BOND              : angle       2.09972 (   16)
  hydrogen bonds       : bond        0.03640 (   53)
  hydrogen bonds       : angle       7.18698 (  129)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8584 (pm20) cc_final: 0.7462 (tp30)
REVERT: B  354 ASN cc_start: 0.9237 (t0) cc_final: 0.8879 (t0)
REVERT: B  356 LYS cc_start: 0.9204 (tppt) cc_final: 0.8678 (tppt)
REVERT: B  422 ASN cc_start: 0.9355 (p0) cc_final: 0.9105 (p0)
REVERT: B  423 TYR cc_start: 0.8889 (t80) cc_final: 0.8512 (t80)
REVERT: B  489 TYR cc_start: 0.7878 (m-80) cc_final: 0.7596 (m-80)
REVERT: D  340 GLU cc_start: 0.9045 (mp0) cc_final: 0.8779 (mp0)
REVERT: D  358 ILE cc_start: 0.8662 (mp) cc_final: 0.8438 (mp)
REVERT: D  394 ASN cc_start: 0.9075 (t0) cc_final: 0.8181 (p0)
REVERT: D  402 ILE cc_start: 0.9006 (tp) cc_final: 0.8634 (tp)
REVERT: D  406 GLU cc_start: 0.8910 (pm20) cc_final: 0.8452 (pm20)
REVERT: D  473 TYR cc_start: 0.9034 (t80) cc_final: 0.8599 (t80)
REVERT: D  509 ARG cc_start: 0.8344 (ttm110) cc_final: 0.8119 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 121
  average time/residue: 0.0857
  time to fit residues: 12.1336
Evaluate side-chains
  95 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.081 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 26 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 21 optimal weight:   10.0000
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   chunk 20 optimal weight:    6.9990
   chunk 25 optimal weight:    0.8980
   chunk 0 optimal weight:   20.0000
   chunk 35 optimal weight:    2.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 360 ASN
D 474 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.111097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.092780 restraints weight = 14016.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.095481 restraints weight = 8759.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.097422 restraints weight = 6170.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.098865 restraints weight = 4701.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.099861 restraints weight = 3794.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7362
moved from start:          0.6030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3633  Z= 0.135
  Angle     :  0.739   8.921   4946  Z= 0.374
  Chirality :  0.047   0.232    509
  Planarity :  0.005   0.050    644
  Dihedral  :  5.885  22.798    492
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 14.12 %
    Favored  : 84.71 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.27 %
    Favored  : 99.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.29 (0.39), residues: 425
  helix: -3.26 (0.62), residues: 41
  sheet: -0.92 (0.59), residues: 73
  loop : -2.55 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 403 
 TYR   0.024   0.002   TYR B 421 
 PHE   0.020   0.002   PHE D 400 
 TRP   0.013   0.001   TRP D 436 
 HIS   0.002   0.000   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 3625)
  covalent geometry    : angle       0.73374 ( 4930)
  SS BOND              : bond        0.00374 (    8)
  SS BOND              : angle       1.70726 (   16)
  hydrogen bonds       : bond        0.03552 (   53)
  hydrogen bonds       : angle       7.02863 (  129)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  850 Ramachandran restraints generated.
    425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.163 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 GLU cc_start: 0.8515 (pm20) cc_final: 0.7425 (tp30)
REVERT: B  354 ASN cc_start: 0.9177 (t0) cc_final: 0.8893 (t0)
REVERT: B  356 LYS cc_start: 0.9121 (tppt) cc_final: 0.8675 (tppt)
REVERT: B  388 ASN cc_start: 0.6967 (t0) cc_final: 0.6663 (m110)
REVERT: B  403 ARG cc_start: 0.7355 (mpp-170) cc_final: 0.6867 (mtm-85)
REVERT: D  340 GLU cc_start: 0.9034 (mp0) cc_final: 0.8770 (mp0)
REVERT: D  394 ASN cc_start: 0.8930 (t0) cc_final: 0.8233 (p0)
REVERT: D  402 ILE cc_start: 0.8934 (tp) cc_final: 0.8607 (tp)
REVERT: D  406 GLU cc_start: 0.8948 (pm20) cc_final: 0.8389 (pm20)
REVERT: D  409 GLN cc_start: 0.8894 (mt0) cc_final: 0.8682 (tt0)
REVERT: D  473 TYR cc_start: 0.8937 (t80) cc_final: 0.8409 (t80)
REVERT: D  509 ARG cc_start: 0.8179 (ttm110) cc_final: 0.7951 (ttm170)
REVERT: D  516 GLU cc_start: 0.7805 (tp30) cc_final: 0.6917 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 126
  average time/residue: 0.0870
  time to fit residues: 12.6915
Evaluate side-chains
  98 residues out of total 375 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 42
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 41 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 17 optimal weight:   10.0000
   chunk 24 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 30 optimal weight:    6.9990
   chunk 18 optimal weight:    0.7980
   chunk 21 optimal weight:   20.0000
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
D 474 GLN
** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.113435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.094482 restraints weight = 13339.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.097292 restraints weight = 8385.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.099264 restraints weight = 5931.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.100731 restraints weight = 4535.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.101756 restraints weight = 3671.575|
|-----------------------------------------------------------------------------|
r_work (final): 0.3537
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
moved from start:          0.6329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3633  Z= 0.132
  Angle     :  0.768  12.647   4946  Z= 0.382
  Chirality :  0.048   0.238    509
  Planarity :  0.005   0.050    644
  Dihedral  :  5.843  22.573    492
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  1.18 %
    Allowed  : 13.41 %
    Favored  : 85.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.39), residues: 425
  helix: -3.22 (0.63), residues: 41
  sheet: -0.69 (0.60), residues: 70
  loop : -2.52 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 403 
 TYR   0.020   0.002   TYR B 421 
 PHE   0.034   0.002   PHE B 375 
 TRP   0.015   0.001   TRP D 436 
 HIS   0.001   0.000   HIS D 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 3625)
  covalent geometry    : angle       0.76431 ( 4930)
  SS BOND              : bond        0.00282 (    8)
  SS BOND              : angle       1.56637 (   16)
  hydrogen bonds       : bond        0.03341 (   53)
  hydrogen bonds       : angle       6.93246 (  129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 837.49 seconds
wall clock time: 15 minutes 9.64 seconds (909.64 seconds total)